annotate wrapper.sh @ 0:c33d93683a09 draft

Uploaded
author davidvanzessen
date Thu, 13 Oct 2016 10:52:24 -0400
parents
children faae21ba5c63
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1 #!/bin/bash
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2 #set -e
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4 input=$1
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5 method=$2
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6 log=$3 #becomes the main html page at the end
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7 outdir=$4
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8 output="$outdir/index.html" #copied to $log location at the end
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9 title=$5
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10 include_fr1=$6
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11 functionality=$7
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12 unique=$8
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13 naive_output_ca=$9
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14 naive_output_cg=${10}
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15 naive_output_cm=${11}
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16 filter_unique=${12}
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17 class_filter=${13}
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18 empty_region_filter=${14}
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19 mkdir $outdir
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20
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21 tar -xzf $dir/style.tar.gz -C $outdir
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22
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23 echo "---------------- read parameters ----------------"
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24 echo "---------------- read parameters ----------------<br />" > $log
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25
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26 echo "unpacking IMGT file"
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27
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28 type="`file $input`"
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29 if [[ "$type" == *"Zip archive"* ]] ; then
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30 echo "Zip archive"
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31 echo "unzip $input -d $PWD/files/"
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32 unzip $input -d $PWD/files/
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33 elif [[ "$type" == *"XZ compressed data"* ]] ; then
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34 echo "ZX archive"
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35 echo "tar -xJf $input -C $PWD/files/"
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36 mkdir -p $PWD/files/$title
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37 tar -xJf $input -C $PWD/files/$title
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38 fi
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39
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40 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
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41 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
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42 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
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43 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
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44 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
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45 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
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46 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
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47
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48 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
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49 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
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50 else
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51 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
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52 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
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53 fi
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54
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55 echo "---------------- class identification ----------------"
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56 echo "---------------- class identification ----------------<br />" >> $log
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57
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58 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
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59
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60 echo "---------------- merge_and_filter.r ----------------"
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61 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
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62
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63 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
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64
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65 echo "---------------- creating new IMGT zips ----------------"
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66 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
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67
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68 mkdir $outdir/new_IMGT
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69
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70 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
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71 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
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72 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
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73 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
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74 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
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75 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
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76 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
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77 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
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78 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
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79 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
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80
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81 mkdir $outdir/new_IMGT_IGA
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82 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
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83
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84 mkdir $outdir/new_IMGT_IGA1
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85 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
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86
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87 mkdir $outdir/new_IMGT_IGA2
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88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
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89
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90 mkdir $outdir/new_IMGT_IGG
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91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
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92
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93 mkdir $outdir/new_IMGT_IGG1
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94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
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95
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96 mkdir $outdir/new_IMGT_IGG2
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97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
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98
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99 mkdir $outdir/new_IMGT_IGG3
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100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
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101
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102 mkdir $outdir/new_IMGT_IGG4
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103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
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104
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105 mkdir $outdir/new_IMGT_IGM
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106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
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107
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108 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
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109
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110 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
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111 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
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112 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
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113
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114 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
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115 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
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116 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
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117 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
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118 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
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119
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120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
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121
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122
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123 tmp="$PWD"
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124 cd $outdir/new_IMGT/ #tar weirdness...
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125 tar -cJf ../new_IMGT.txz *
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126
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127 cd $outdir/new_IMGT_IGA/
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128 tar -cJf ../new_IMGT_IGA.txz *
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129
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130 cd $outdir/new_IMGT_IGA1/
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131 tar -cJf ../new_IMGT_IGA1.txz *
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132
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133 cd $outdir/new_IMGT_IGA2/
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134 tar -cJf ../new_IMGT_IGA2.txz *
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135
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136 cd $outdir/new_IMGT_IGG/
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137 tar -cJf ../new_IMGT_IGG.txz *
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138
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139 cd $outdir/new_IMGT_IGG1/
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140 tar -cJf ../new_IMGT_IGG1.txz *
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141
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142 cd $outdir/new_IMGT_IGG2/
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143 tar -cJf ../new_IMGT_IGG2.txz *
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144
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145 cd $outdir/new_IMGT_IGG3/
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146 tar -cJf ../new_IMGT_IGG3.txz *
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147
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148 cd $outdir/new_IMGT_IGG4/
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149 tar -cJf ../new_IMGT_IGG4.txz *
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150
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151 cd $outdir/new_IMGT_IGM/
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152 tar -cJf ../new_IMGT_IGM.txz *
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153
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154 cd $tmp
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155
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156 echo "---------------- shm_csr.r ----------------"
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157 echo "---------------- shm_csr.r ----------------<br />" >> $log
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158
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159 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched"
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160 echo "R mutation analysis"
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161 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
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162
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163
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164 echo "---------------- shm_csr.py ----------------"
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165 echo "---------------- shm_csr.py ----------------<br />" >> $log
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166
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167 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
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168
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169 echo "---------------- aa_histogram.r ----------------"
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170 echo "---------------- aa_histogram.r ----------------<br />" >> $log
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171
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172 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM" $outdir/ 2>&1
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173 if [ -e "$outdir/aa_histogram_.png" ]; then
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174 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
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175 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
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davidvanzessen
parents:
diff changeset
176 fi
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davidvanzessen
parents:
diff changeset
177
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davidvanzessen
parents:
diff changeset
178 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM)
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davidvanzessen
parents:
diff changeset
179
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davidvanzessen
parents:
diff changeset
180 funcs=(sum mean median)
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davidvanzessen
parents:
diff changeset
181 funcs=(sum)
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davidvanzessen
parents:
diff changeset
182
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davidvanzessen
parents:
diff changeset
183 echo "---------------- sequence_overview.r ----------------"
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davidvanzessen
parents:
diff changeset
184 echo "---------------- sequence_overview.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
185
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davidvanzessen
parents:
diff changeset
186 mkdir $outdir/sequence_overview
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davidvanzessen
parents:
diff changeset
187
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davidvanzessen
parents:
diff changeset
188 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
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davidvanzessen
parents:
diff changeset
189
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davidvanzessen
parents:
diff changeset
190 echo "<table border='1'>" > $outdir/base_overview.html
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davidvanzessen
parents:
diff changeset
191
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davidvanzessen
parents:
diff changeset
192 while IFS=$'\t' read ID class seq A C G T
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davidvanzessen
parents:
diff changeset
193 do
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davidvanzessen
parents:
diff changeset
194 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
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davidvanzessen
parents:
diff changeset
195 done < $outdir/sequence_overview/ntoverview.txt
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davidvanzessen
parents:
diff changeset
196
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davidvanzessen
parents:
diff changeset
197 echo "<html><center><h1>$title</h1></center>" > $output
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davidvanzessen
parents:
diff changeset
198 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
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davidvanzessen
parents:
diff changeset
199 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
200 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
201 echo "<script type='text/javascript' src='script.js'></script>" >> $output
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davidvanzessen
parents:
diff changeset
202 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
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davidvanzessen
parents:
diff changeset
203 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
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davidvanzessen
parents:
diff changeset
204
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davidvanzessen
parents:
diff changeset
205 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
206 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
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davidvanzessen
parents:
diff changeset
207 total_count=$((matched_count + unmatched_count))
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davidvanzessen
parents:
diff changeset
208 perc_count=$((unmatched_count / total_count * 100))
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davidvanzessen
parents:
diff changeset
209 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
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davidvanzessen
parents:
diff changeset
210 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
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davidvanzessen
parents:
diff changeset
211
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davidvanzessen
parents:
diff changeset
212 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
213 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
214 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
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davidvanzessen
parents:
diff changeset
215
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davidvanzessen
parents:
diff changeset
216 echo "---------------- main tables ----------------"
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davidvanzessen
parents:
diff changeset
217 echo "---------------- main tables ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
218
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davidvanzessen
parents:
diff changeset
219 echo "<div class='tabber'>" >> $output
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davidvanzessen
parents:
diff changeset
220 echo "<div class='tabbertab' title='SHM Overview'>" >> $output
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davidvanzessen
parents:
diff changeset
221
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davidvanzessen
parents:
diff changeset
222 for func in ${funcs[@]}
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davidvanzessen
parents:
diff changeset
223 do
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davidvanzessen
parents:
diff changeset
224
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davidvanzessen
parents:
diff changeset
225 echo "---------------- $func table ----------------"
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davidvanzessen
parents:
diff changeset
226 echo "---------------- $func table ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
227
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davidvanzessen
parents:
diff changeset
228 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
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davidvanzessen
parents:
diff changeset
229
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davidvanzessen
parents:
diff changeset
230 echo "---------------- pattern_plots.r ----------------"
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davidvanzessen
parents:
diff changeset
231 echo "---------------- pattern_plots.r ----------------<br />" >> $log
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davidvanzessen
parents:
diff changeset
232
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davidvanzessen
parents:
diff changeset
233 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
234
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davidvanzessen
parents:
diff changeset
235 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
236 echo "<thead><tr><th>info</th>" >> $output
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davidvanzessen
parents:
diff changeset
237
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davidvanzessen
parents:
diff changeset
238 if [ "${class_filter}" != "101_101" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
239
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davidvanzessen
parents:
diff changeset
240 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
241 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
242 tmp=`cat $outdir/${gene}_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
243 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
244 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
245
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davidvanzessen
parents:
diff changeset
246 tmp=`cat $outdir/all_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
247 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
248 tmp=`cat $outdir/unmatched_${func}_n.txt`
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davidvanzessen
parents:
diff changeset
249 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
250
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davidvanzessen
parents:
diff changeset
251 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
252 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
253 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
254 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
255 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
256 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
257 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
258 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
259 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
260 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
261
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
262 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
263 tmp=`cat $outdir/unmatched_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
264 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
265
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
266 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
267 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
268 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
269 echo "<tr><td>$name</td><td>${unx}/${uny}</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
270 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
271 echo "<tr><td>$name</td><td>${unz}%</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
273 echo "<tr><td>$name</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
274 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
275 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
276
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
278 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
279 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
280 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
281
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
282 echo "<img src='plot1.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
283 echo "<img src='plot2.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
284 echo "<img src='plot3.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
285
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
286 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
288 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
290
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
291 echo "<div class='tabbertab' title='SHM Frequency'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
294 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 echo "<img src='scatter.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
297 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
299 echo "<img src='frequency_ranges.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
301
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
303
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
304 echo "<div class='tabbertab' title='Transition tables'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
305
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
308 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
309 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
310 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
311 echo "<td><h1>${gene}</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
312 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
313 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
314 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
315 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
316 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
317 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
320 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
321 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
324 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
325 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
329 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
330
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
331 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
332 echo "<td><h1>All</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
333 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
334 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
336 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
338 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
342 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
343 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
346 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
354
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
355 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
356
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357 if [ -a $outdir/aa_histogram.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 echo "<img src='aa_histogram.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 if [ -a $outdir/IGA.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378 if [ -a $outdir/IGG.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 echo "---------------- change-o MakeDB ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387 mkdir $outdir/change_o
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 tmp="$PWD"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391 cd $outdir/change_o
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
396 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
397
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
398 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
399
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
400 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
401 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
403 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
405 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
407
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
408 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
409 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
410 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
411 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
412 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
413 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
414 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
415
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
416 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
417 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
418 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
419 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
420 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
421 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
422 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
423
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
424 PWD="$tmp"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
425
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
426 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
427
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
428 function clonality_table {
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
429 local infile=$1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
430 local outfile=$2
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
431
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
432 echo "<table class='pure-table pure-table-striped'>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
433 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
434
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
435 first='true'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
436
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
437 while read size clones seqs
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
438 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
439 if [[ "$first" == "true" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
440 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
441 continue
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
442 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
443 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
444 done < $infile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
445
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
446 echo "</table>" >> $outfile
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
447 }
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
448 echo "<div class='tabber'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
449
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
450 echo "<div class='tabbertab' title='All'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
451 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
452 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
453
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
454 echo "<div class='tabbertab' title='Ca'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
455 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
456 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
457
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
458 echo "<div class='tabbertab' title='Cg'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
459 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
460 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
461
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
462 echo "<div class='tabbertab' title='Cm'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
463 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
464 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
465
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
466 echo "<div class='tabbertab' title='Overview'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
467 cat "$outdir/sequence_overview/index.html" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
468 echo "</div>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
469
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
470
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
471 echo "</div>" >> $output #clonality tabber end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
472
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
473 echo "</div>" >> $output #clonality tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
474
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
475 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
476
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
477 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
478 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
479 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
480 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
481 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
482 echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
483 echo "<tr><td>The data used to generate the second SHM Overview plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
484 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
485 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
486
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
487 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
488 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
489 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
490
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
491
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
492 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
493 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
494 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
495 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
496 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
497
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
498 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
499
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
500 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
501 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
502 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
503 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
504 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
505 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
506 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
507 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
508
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
509 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
510 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
511 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
512 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
513 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
514 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
515 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
516 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
517 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
518 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
519
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
520 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
521 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
522 echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
523 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
524 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
525 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
526 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
527 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
528
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
529 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
530
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
531 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
532
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
533 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
534
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
536
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
537 echo "---------------- baseline ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
538 echo "---------------- baseline ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539 tmp="$PWD"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
540
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
541 mkdir $outdir/baseline
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
542
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
543
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
544 mkdir $outdir/baseline/IGA_IGG_IGM
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
545 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
546 cd $outdir/baseline/IGA_IGG_IGM
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
547 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
548 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549 echo "No sequences" > "$outdir/baseline.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
550 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
551
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
552 mkdir $outdir/baseline/IGA
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
553 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
554 cd $outdir/baseline/IGA
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
555 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
556 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
557 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
558 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
559
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
560 mkdir $outdir/baseline/IGG
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
561 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
562 cd $outdir/baseline/IGG
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
563 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
564 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
565 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
566 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
567
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
568 mkdir $outdir/baseline/IGM
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
569 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
570 cd $outdir/baseline/IGM
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
571 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
572 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
573 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
574 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
575
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
576 cd $tmp
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
577
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
578 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
579 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
580
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
581 if [[ "$naive_output" != "None" ]]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
582 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
583 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
584 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
585 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
586 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
587
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
588 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
589
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
590 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
591
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
592 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
593 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
594 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
595 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
596 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
597 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
598 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
599 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
600 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
601 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
602 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
603 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
604 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
605 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
606
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
607 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
608
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
609
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
610 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
611 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
612
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
613
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
614
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
615
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
616
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
617
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
618
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
619
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
620
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
621
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
622
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
623
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
624
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
625
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
626
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
627
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
628
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
629
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
630
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
631
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
632